Characterization and validation of TaAGL66, a gene related to fertility conversion of wheat in the presence of Aegilops kotschyi cytoplasm.

MAIN CONCLUSION: TaAGL66, a MADS-box transcription factor highly expressed in fertile anthers of KTM3315A, regulates anther and/or pollen development, as well as male fertility in wheat with Aegilops kotschyi cytoplasm. Male sterility, as a string of sophisticated biological processes in higher plants, is commonly regulated by transcription factors (TFs). Among them, MADS-box TFs are mainly participated in the processes of floral organ formation and pollen development, which are tightly related to male sterility, but they have been little studied in the reproductive development in wheat. In our study, TaAGL66, a gene that was specifically expressed in spikes and highly expressed in fertile anthers, was identified by RNA sequencing and the expression profiles data of these genes, and qRT-PCR analyses, which was localized to the nucleus. Silencing of TaAGL66 under fertility condition in KTM3315A, a thermo-sensitive male sterile line with Ae. kotschyi cytoplasm, displayed severe fertility reduction, abnormal anther dehiscence, defective pollen development, decreased viability, and low seed-setting. It can be concluded that TaAGL66 plays an important role in wheat pollen development in the presence of Ae. kotschyi cytoplasm, providing new insights into the utilization of male sterility.

Identification and validation of major-effect quantitative trait locus QMS-5B associated with male sterility in photo-thermo-sensitive genic male sterile wheat.

KEY MESSAGE: QMS-5B, a major QTL for photo-thermo-sensitive genic male sterility in wheat, was fine mapped in a 2.15 Mb region harboring a serine/threonine protein kinase gene TraesCS5B03G0887500, which was the most likely candidate gene. Genic male sterility is an essential trait in the utilization of heterosis and hybrid seed production for wheat. Currently, genic male sterile genes have been reported in wheat mutants, but the sterile genes controlling photo-thermo-sensitive genic male sterility in wheat have not been studied systematically. Here, 235 doubled haploid lines derived from a cross between photo-thermo-sensitive genic male sterile line BS462 and its restorer line CP279 were used to map male sterile gene by GenoBaits® Wheat 100 K Panel, bulked segregant exome sequencing (BSE-Seq) and wheat 660 K array. As a result, the major stable QTL on chromosome 5B, QMS-5B, was identified in all four environments, accounting for 7.3-36.4% of the phenotypic variances. Ulteriorly, QMS-5B was delimited to an approximate 2.15 Mb physical interval between KASP-5B5 and KASP-5B6 using kompetitive allele-specific PCR (KASP) markers. Within the interval, twenty-nine high-confidence genes were predicted according to Chinese Spring RefSeq v2.1. TraesCS5B03G0887500, encoding a serine/threonine protein kinase, was identified as the most likely candidate gene for QMS-5B based on weighted gene co-expression network analysis. Expression analysis confirmed that TraesCS5B03G0887500 was significantly differentially expressed in anthers of BS462 and CP279 at different stages under fertile and sterile environments. In addition, flanking KASP marker KASP-5B6 can effectively genotype male sterile lines and restorer lines, and can be used for molecular marker-assisted selection. This study provides insights into for exploring the mechanism of photo-thermo-sensitive genic male sterility in wheat.

Denoising odontocete echolocation clicks using a hybrid model with convolutional neural network and long short-term memory network.

Ocean noise negatively influences the recording of odontocete echolocation clicks. In this study, a hybrid model based on the convolutional neural network (CNN) and long short-term memory (LSTM) network-called a hybrid CNN-LSTM model-was proposed to denoise echolocation clicks. To learn the model parameters, the echolocation clicks were partially corrupted by adding ocean noise, and the model was trained to recover the original echolocation clicks. It can be difficult to collect large numbers of echolocation clicks free of ambient sea noise for training networks. Data augmentation and transfer learning were employed to address this problem. Based on Gabor functions, simulated echolocation clicks were generated to pre-train the network models, and the parameters of the networks were then fine-tuned using odontocete echolocation clicks. Finally, the performance of the proposed model was evaluated using synthetic data. The experimental results demonstrated the effectiveness of the proposed model for denoising two typical echolocation clicks-namely, narrowband high-frequency and broadband echolocation clicks. The denoising performance of hybrid models with the different number of convolution and LSTM layers was evaluated. Consequently, hybrid models with one convolutional layer and multiple LSTM layers are recommended, which can be adopted for denoising both types of echolocation clicks.

Rfd1, a restorer to the Aegilops juvenalis cytoplasm, functions in fertility restoration of wheat cytoplasmic male sterility.

Cytoplasmic male sterility (CMS) is a crucial means for the utilization of heterosis, which is of great significance for improving the yield and quality of hybrids. Currently, fertility restoration has been extensively investigated in crops, but fertility restoration of CMS wheat with Aegilops juvenalis cytoplasm is poorly understood. Here, a backcross population BC1F1 derived from a cross between the male-sterile line Ju706A, its maintainer line 706B, and restorer line LK783 was used to map the Rfd1 locus by bulked segregant analysis and wheat 660K single nucleotide polymorphism genotyping. Ju706A displayed complete male sterility, and its fertility can be restored by LK783 with a pair of dominant genes Rfd1Rfd1. The locus was located to a 2.4 Mb region on chromosome 1BS by markers AX-174254104 and AX-111201011. Combined with transcriptomic analysis and quantitative real-time PCR assay, TraesCS1B02G197400LC, the most likely candidate gene for Rfd1, was found to encode a pectinesterase that was localized in the cell wall, and was highly expressed in fertile anthers. The silencing of Rfd1 resulted in decreased fertility, and heterogeneous expression of Rfd1 promoted pollen germination and affected vegetative growth. This implies that Rfd1 is required for anther or pollen development and male fertility in CMS wheat with Ae. juvenalis cytoplasm. Furthermore, a 7 bp deletion in Ju706A was employed to develop a specific marker, Xnwafu1, for molecular marker-assisted selection of restorers. This study provides a new understanding for exploring the fertility restoration mechanism of CMS.

Comparative Transcriptome Analysis Reveals Key Insights into Fertility Conversion in the Thermo-Sensitive Cytoplasmic Male Sterile Wheat.

Thermo-sensitive cytoplasmic male sterility (TCMS) plays a crucial role in hybrid production and hybrid breeding; however, there are few studies on molecular mechanisms related to anther abortion in the wheat TCMS line. In this study, FA99, a new wheat thermo-sensitive cytoplasmic male sterility line, was investigated. Fertility conversion analysis showed that FA99 was mainly controlled by temperature, and the temperature-sensitive stage was pollen mother cell formation to a uninucleate stage. Further phenotypic identification and paraffin section showed that FA99 was characterized by indehiscent anthers and aborted pollen in a sterile environment and tapetum was degraded prematurely during the tetrad period, which was the critical abortion period of FA99. The contents of O2-, H2O2, MDA and POD were significantly changed in FA99 under a sterile environment by the determination of physiological indexes. Furthermore, through transcriptome analysis, 252 differentially expressed genes were identified, including 218 downregulated and 34 upregulated genes. Based on KOG function classification, GO enrichment and KEGG pathways analysis, it was evident that significant transcriptomic changes in FA99 under different fertility environments, and the major differences were "phenylalanine metabolism", "phenylpropanoid biosynthesis", "cutin, suberine and wax biosynthesis", "phenylalanine, tyrosine and tryptophan biosynthesis" and "citrate cycle (TCA cycle)". Finally, we proposed an intriguing transcriptome-mediated pollen abortion and male sterility network for FA99. These findings provided data on the molecular mechanism of fertility conversion in thermo-sensitive cytoplasmic male sterility wheat.

The transcription factor TaGAMYB modulates tapetum and pollen development of TGMS wheat YanZhan 4110S via the gibberellin signaling.

Male reproductive development in higher plants experienced a series of complex biological processes, which can be regulated by Gibberellins (GA). The transcriptional factor GAMYB is a crucial component of GA signaling in anther development. However, the mechanism of GAMYB in wheat male reproduction is less understood. Here, we found that the thermo-sensitive genic male sterilitywheat line YanZhan 4110S displayed delayed tapetum programmed cell death and pollen abortive under the hot temperature stress. Combined with RNA-Sequencing data analysis, TaGAMYB associated with fertility conversion was isolated, which was located in the nucleus and highly expressed in fertility anthers. The silencing of TaGAMYB in wheat displayed fertility decline, defects in tapetum, pollen and exine formation, where the abortion characteristics were the same as YanZhan 4110S. In addition, either hot temperature or GA3 treatment in YanZhan 4110S caused the downregulation of TaGAMYB at binucleate stage and trinucleate stage, as well as fertility decrease. Further, the transcription factor TaWRKY2 significantly changed under GA3-treatment and directly interacted with the TaGAMYB promoter by W-box cis-element. Therefore, we suggested that TaGAMYB may be essential for anther development and male fertility, and GA3 activates TaGAMYB by TaWRKY2 to regulate fertility in wheat.

The gene TaPG encoding a polygalacturonase is critical for pollen development and male fertility in thermo-sensitive cytoplasmic male-sterility wheat.

Thermo-sensitive cytoplasmic male sterility is of great significance to heterosis and hybrid seed production in wheat. Consequently, it is worthwhile to research the genes associated with male sterility. Although polygalacturonases (PGs) have been studied to play a crucial role in male reproduction of many plants, their functions in the reproductive development of wheat remain unclear. Here, TaPG (TraesCS7A02G404900) encoding a polygalacturonase was isolated from the anthers of KTM3315A, a wheat thermo-sensitive cytoplasmic male sterile with Aegilops kotschyi cytoplasm. Expression pattern analyses showed that TaPG was strongly expressed in fertile anthers and its protein was localized in the cell wall. Further verification via barley stripe mosaic virus revealed that the silencing of TaPG exhibited abnormal anthers, premature degradation of tapetum, pollen abortion, and defective pollen wall formation, resulting in the declination of fertility. Conclusively, our research suggested that TaPG contributed to the pollen development and male fertility, which will provide a novel insight into the fertility conversion of thermo-sensitive cytoplasmic male sterility in wheat.

Comprehensive analysis of LIM gene family in wheat reveals the involvement of TaLIM2 in pollen development.

LIM domain proteins were involved in organizing the cytoskeleton, adjusting the metabolism and gene expression, some of them were specific express in pollen. LIM gene family in plants were studied in sunflower, tobacco, foxtail millet, rape, rice and Arabidopsis thaliana, however, it has not been investigated in wheat to date. In the present study, we totally characterized 29 TaLIM genes through genome-wide analysis, which were divided into two categories and five subclasses according to phylogenetic analysis. RNA-Seq analysis indicated the expression patterns of TaLIM genes have specific temporal and spatial characteristics, especially TaLIM2 was highly expressed in fertility anthers. Phenotypic and cytological of BSMV: TaLIM2 showed that it had defects in the later stage of pollen development and germination, which further testified that TaLIM2 was closely related to fertility conversion. These findings will be useful for functional analysis of LIM genes in wheat fertility and contribute to hybrid wheat breeding.

Automated classification of tursiops aduncus whistles based on a depth-wise separable convolutional neural network and data augmentation.

Whistle classification plays an essential role in studying the habitat and social behaviours of cetaceans. We obtained six categories of sweep whistles of two Tursiops aduncus individual signals using the passive acoustic mornitoring technique over a period of eight months in the Xiamen area. First, we propose a depthwise separable convolutional neural network for whistle classification. The proposed model adopts the depthwise convolution combined with the followed point-by-point convolution instead of the conventional convolution. As a result, it brings a better classification performance in sample sets with relatively independent features between different channels. Meanwhile, it leads to less computational complexity and fewer model parameters. Second, in order to solve the problem of an imbalance in the number of samples under each whistle category, we propose a random series method with five audio augmentation algorithms. The generalization ability of the trained model was improved by using an opening probability for each algorithm and the random selection of each augmentation factor within specific ranges. Finally, we explore the effect of the proposed augmentation method on the performance of our proposed architecture and find that it enhances the accuracy up to 98.53% for the classification of Tursiops aduncus whistles.

Baseline assessment of ocean ambient noise in the western Clarion Clipperton Zone, Pacific Ocean.

Ocean noise in the western Clarion Clipperton Zone, Pacific Ocean was recorded for 5 min every hour during 2017 and 2018, at a depth of 300 m. The monthly and hourly mean spectrum levels in the 20-1000 Hz band were calculated, along with their skewness, kurtosis, percentile distributions, and spectral probability densities. The high noise levels at low frequencies generated from distant shipping and vocalizations of whales were found to range between 70 and 100 dB (<100 Hz) and 64-93 dB (100-200 Hz), respectively. The noise levels at high frequencies (>200 Hz), which are typically dominated by wind, were found to be low, ranging from 53 to 75 dB. At frequencies above 200 Hz, noise levels in winter were approximately 5 dB higher than those in summer, consistent with the seasonal variations in wind speed. Fin whales, blue whales, and fishes also potentially contributed to variations in the baseline of ambient noise.

Identification and verification of genes related to pollen development and male sterility induced by high temperature in the thermo-sensitive genic male sterile wheat line.

MAIN CONCLUSION: Bioinformatic analysis identified the function of genes regulating wheat fertility. Barley stripe mosaic virus-induced gene silencing verified that the genes TaMut11 and TaSF3 are involved in pollen development and related to fertility conversion. Environment-sensitive genic male sterility is of vital importance to hybrid vigor in crop production and breeding. Therefore, it is meaningful to study the function of the genes related to pollen development and male sterility, which is still not fully understand currently. In this study, YanZhan 4110S, a new thermo-sensitive genic male sterility wheat line, and its near-isogenic line YanZhan 4110 were analyzed. Through comparative transcriptome basic bioinformatics and weighted gene co-expression network to further identify some hub genes, the genes TaMut11 and TaSF3 associated with pollen development and male sterility induced by high-temperature were identified in YanZhan 4110S. Further verification through barley stripe mosaic virus-induced gene silencing elucidated that the silencing of TaMut11 and TaSF3 caused pollen abortion, finally resulting in the declination of fertility. These findings provided data on the abortive mechanism in environment-sensitive genic male sterility wheat.

Identification and validation of genetic locus Rfk1 for wheat fertility restoration in the presence of Aegilops kotschyi cytoplasm.

KEY MESSAGE: Major fertility restorer locus for Aegilops kotschyi cytoplasm in wheat, Rfk1, was mapped to chromosome arm 1BS. Most likely candidate gene is TraesCS1B02G197400LC, which is predicted to encode a pectinesterase/pectinesterase inhibitor. Cytoplasmic male sterility (CMS) is widely used for heterosis and hybrid seed production in wheat. Genes related to male fertility restoration in the presence of Aegilops kotschyi cytoplasm have been reported, but the fertility restoration-associated gene loci have not been investigated systematically. In this study, a BC1F1 population derived from a backcross between KTP116A, its maintainer line TP116B, and its restorer line LK783 was employed to map fertility restoration by bulked segregant RNA-Seq (BSR-Seq). A major fertility allele restorer locus for Ae. kotschyi cytoplasm in wheat, Rfk1, was mapped to chromosome arm 1BS, and it was contributed by LK783. Morphological and cytological studies showed that male fertility restoration occurred mainly after the late uninucleate stage. Based on simple sequence repeat and single-nucleotide polymorphism genotyping, the gene locus was located between Xnwafu_6 and Xbarc137 on chromosome arm 1BS. To further isolate the specific region, six Kompetitive allele-specific polymerase chain reaction markers derived from BSR-Seq were developed to delimit Rfk1 within physical intervals of 26.0 Mb. After searching for differentially expressed genes within the candidate interval in the anthers and sequencing analysis, TraesCS1B02G197400LC was identified as a candidate gene for Rfk1 and it was predicted to encode a pectinesterase/pectinesterase inhibitor. Expression analysis also confirmed that it was specifically expressed in the anthers, and its expression level was higher in fertile lines compared with sterile lines. Thus, TraesCS1B02G197400LC was identified as the most likely candidate gene for Rfk1, thereby providing insights into the fertility restoration mechanism for K-type CMS in wheat.

Comprehensive analysis of polygalacturonase gene family highlights candidate genes related to pollen development and male fertility in wheat (Triticum aestivum L.).

MAIN CONCLUSION: Four polygalacturonase gene family members were highlighted that contribute to elucidate the roles of polygalacturonase during the fertility conversion process in male-sterile wheat. Polygalacturonase (PG) belongs to a large family of hydrolases with important functions in cell separation during plant growth and development via the degradation of pectin. Specific expressed PGs in anthers may be significant for male sterility research and hybrid wheat breeding, but they have not been characterized in wheat (Triticum aestivum L.). In this study, we systematically studied the PG gene family using the latest published wheat reference genomic information. In total, 113 wheat PG genes were identified, which could be classified into six categories A-F according to their structure characteristics and phylogenetic comparisons with Arabidopsis and rice. Polyploidy and segmental duplications in wheat were proved to be mainly responsible for the expansion of the wheat PG gene family. RNA-seq showed that TaPGs have specific temporal and spatial expression characteristics, in which 12 TaPGs with spike-specific expression patterns were detected by qRT-PCR in different fertility anthers of KTM3315A, a thermo-sensitive cytoplasmic male-sterile wheat. Four of them specific upregulated (TaPG09, TaPG95, and TaPG93) or downregulated (TaPG87) at trinucleate stage of fertile anthers, and further aligning with the homologous in Arabidopsis revealed that they may undertake functions such as anther dehiscence, separation of pollen, pollen development, and pollen tube elongation, thereby inducing male fertility conversion in KTM3315A. These findings facilitate function investigations of the wheat PG gene family and provide new insights into the fertility conversion mechanism in male-sterile wheat.

Evoked-potential audiogram variability in a group of wild Yangtze finless porpoises (Neophocaena asiaeorientalis asiaeorientalis).

Hearing is considered the primary sensory modality of cetaceans and enables their vital life functions. Information on the hearing sensitivity variability within a species obtained in a biologically relevant wild context is fundamental to evaluating potential noise impact and population-relevant management. Here, non-invasive auditory evoked-potential methods were adopted to describe the audiograms (11.2-152 kHz) of a group of four wild Yangtze finless porpoises (Neophocaena asiaeorientalis asiaeorientalis) during a capture-and-release health assessment project in Poyang Lake, China. All audiograms presented a U shape, generally similar to those of other delphinids and phocoenids. The lowest auditory threshold (51-55 dB re 1 µPa) was identified at a test frequency of 76 kHz, which was higher than that observed in aquarium porpoises (54 kHz). The good hearing range (within 20 dB of the best hearing sensitivity) was from approximately 20 to 145 kHz, and the low- and high-frequency hearing cut-offs (threshold > 120 dB re l µPa) were 5.6 and 170 kHz, respectively. Compared with aquarium porpoises, wild porpoises have significantly better hearing sensitivity at 32 and 76 kHz and worse sensitivity at 54, 108 and 140 kHz. The audiograms of this group can provide a basis for better understanding the potential impact of anthropogenic noise.

Behavioral responses of two captive bottlenose dolphins (Tursiops truncatus) to a continuous 50 kHz tone.

At present, the fundamental frequencies of signals of most commercially available acoustic alarms to deter small cetaceans are below 20 kHz, but it is not well ascertained whether higher frequencies have a deterrent effect on bottlenose dolphins (Tursiops truncatus). Two captive bottlenose dolphins housed in a floating pen were subjected to a continuous pure tone at 50 kHz with a source level of 160 ± 2 dB (re 1 µPa, rms). The behavioral responses of dolphins were judged by comparing surfacing distance relative to the sound source, number of surfacings, and number of echolocation clicks produced, during forty 15 min baseline periods with forty 15 min test periods (four sessions per day, 40 sessions in total). On all 10 study days, surfacing distance and the number of surfacings increased while click production decreased during broadcasts of test sound. The avoidance threshold sound pressure level for a continuous 50 kHz tone for the bottlenose dolphins, in the context of this study, was estimated to be 144 ± 2 dB (re 1 µPa, rms). The results indicated that a continuous 50 kHz tonal signal can deter bottlenose dolphins from an area.